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‎README.md‎

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# MD Akkas Ali — Academic Website
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A responsive academic portfolio designed for GitHub Pages.
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## Content scope
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- The September 2025 AHA biosketch is the authority for positions, awards, presentations, and selected publications.
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- Only published findings and public conference abstracts are described.
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- Portrait and award images are temporarily referenced from the existing Google Site and should later be replaced with optimized local originals.
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## Preview locally
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```bash
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python3 -m http.server 8000
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```
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Open `http://localhost:8000` from this directory.
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## Publish with GitHub Pages
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1. Create a public repository named `mdakkasali.github.io`.
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2. Add these files to the repository's default branch.
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3. Open **Settings → Pages**.
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4. Select **Deploy from a branch**, then select the default branch and `/ (root)`.
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5. The site will appear at `https://mdakkasali.github.io/`.
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## Replace temporary images
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Place optimized images under `assets/images/` and update their `src` values in `index.html`.

‎index.html‎

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<!doctype html>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<meta name="description" content="MD Akkas Ali is a PhD candidate at UAB studying neuroimmunology, brain aging, vascular dementia, and age-associated CD8+ T cells.">
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<meta name="theme-color" content="#0a5c42">
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<title>MD Akkas Ali | Neuroimmunology & Brain Aging</title>
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<link rel="preconnect" href="https://fonts.googleapis.com">
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<link rel="preconnect" href="https://fonts.gstatic.com" crossorigin>
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<link href="https://fonts.googleapis.com/css2?family=DM+Sans:wght@400;500;600;700&family=Newsreader:opsz,wght@6..72,500;6..72,600&display=swap" rel="stylesheet">
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<link rel="stylesheet" href="styles.css">
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<script type="application/ld+json">
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{
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"@context": "https://schema.org",
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"@type": "Person",
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"name": "MD Akkas Ali",
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"jobTitle": "PhD Candidate and Graduate Research Assistant",
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"affiliation": {
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"@type": "CollegeOrUniversity",
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"name": "University of Alabama at Birmingham"
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},
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"url": "https://mdakkasali.github.io/",
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"sameAs": [
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"https://github.com/mdakkasali/",
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"https://scholar.google.com/citations?user=-qIZ0AgAAAAJ&hl=en",
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"https://orcid.org/0000-0002-3626-3393"
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],
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"knowsAbout": ["Neuroimmunology", "Brain aging", "Vascular dementia", "CD8+ T cells", "Single-cell RNA sequencing", "Spectral flow cytometry"]
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}
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</script>
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</head>
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<body>
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<a class="skip-link" href="#main">Skip to content</a>
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<header class="site-header" id="top">
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<nav class="nav shell" aria-label="Primary navigation">
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<a class="brand" href="#top" aria-label="MD Akkas Ali home">
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<span class="brand-mark" aria-hidden="true">AA</span>
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<span>MD Akkas Ali</span>
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</a>
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<button class="menu-toggle" type="button" aria-expanded="false" aria-controls="nav-links">
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<span></span><span></span><span></span>
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<span class="sr-only">Open navigation</span>
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</button>
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<div class="nav-links" id="nav-links">
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<a href="#research">Research</a>
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<a href="#publications">Publications</a>
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<a href="#experience">Experience</a>
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<a href="#recognition">Recognition</a>
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<a href="#contact">Contact</a>
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</div>
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</nav>
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</header>
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<main id="main">
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<section class="hero">
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<div class="hero-grid shell">
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<div class="hero-copy reveal">
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<p class="eyebrow">Neuroimmunology · Brain aging · Vascular dementia</p>
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<h1>Understanding how aging immune cells reshape the brain.</h1>
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<p class="hero-lede">I am a PhD candidate and graduate research assistant at the University of Alabama at Birmingham, studying how age-associated CD8+ T cells and neuroimmune interactions contribute to vascular cognitive impairment and dementia.</p>
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<div class="hero-actions">
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<a class="button button-primary" href="#research">Explore my research</a>
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<a class="button button-secondary" href="https://scholar.google.com/citations?user=-qIZ0AgAAAAJ&hl=en" target="_blank" rel="noopener">Google Scholar</a>
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</div>
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<ul class="hero-meta" aria-label="Current affiliations">
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<li>Department of Pathology</li>
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<li>Graduate Biomedical Sciences</li>
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<li>UAB Heersink School of Medicine</li>
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</ul>
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</div>
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<div class="portrait-wrap reveal">
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<div class="portrait-accent" aria-hidden="true"></div>
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<img class="portrait" src="https://lh3.googleusercontent.com/sitesv/AG8ngQXz2GqDhf732nAOZleNZ1HMW5hHzBmin3mAMqujnFerb7wFyCxC-79IS6rP1uvk2cnfeeirZzLIPYKA99LZjac00KK_H71TNU7Ygn7Fvkxb1HR751eKNI7PT542qUVAsP_S25G7y4mkWXcw0vtYP08XQqLkLPnw0K0FfybtnokvCylDKc79AZ_DpREU=w1280" alt="Portrait of MD Akkas Ali" width="1280" height="1920">
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<div class="portrait-note">
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<strong>Research focus</strong>
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<span>Immune mechanisms of aging and neurovascular disease</span>
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</div>
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</div>
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</div>
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</section>
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<section class="signal-strip" aria-label="Research themes">
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<div class="shell signal-grid">
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<div><span>01</span><strong>Age-associated CD8+ T cells</strong></div>
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<div><span>02</span><strong>Microglia–T cell interactions</strong></div>
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<div><span>03</span><strong>VCID and brain aging</strong></div>
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<div><span>04</span><strong>Single-cell immunology</strong></div>
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</div>
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</section>
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<section class="section intro-section">
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<div class="shell two-column">
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<div>
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<p class="section-kicker">About</p>
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<h2>Connecting vascular dysfunction, immune activation, and dementia.</h2>
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</div>
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<div class="prose">
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<p>My long-term goal is to become an independent investigator in neuroimmunology and develop therapeutic strategies that improve cardiovascular and brain health in aging populations.</p>
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<p>In the laboratory of Dr. Daniel J. Tyrrell, I combine experimental and computational approaches to study immune mechanisms of vascular cognitive impairment and dementia. My training spans rodent models of neurovascular disease, brain immune-cell isolation, neuropathology, single-cell transcriptomics, spectral flow cytometry, and bioinformatics.</p>
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</div>
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</div>
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</section>
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<section class="section section-tint" id="research">
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<div class="shell">
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<div class="section-heading reveal">
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<p class="section-kicker">Current research</p>
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<h2>Immune circuits at the intersection of aging and vascular brain injury.</h2>
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<p>My doctoral work examines published and publicly presented evidence connecting age-associated T-cell states with neuroinflammation and vascular cognitive impairment.</p>
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</div>
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<div class="research-grid">
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<article class="research-card featured reveal">
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<div class="card-number">01</div>
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<div>
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<p class="card-label">Doctoral focus</p>
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<h3>Age-associated CD8+ T cells in the aging brain</h3>
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<p>I investigate how cytotoxic and Granzyme K–associated CD8+ T-cell states accumulate with age and how their interactions with pro-inflammatory microglia may shape the neuroimmune environment in vascular dementia.</p>
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<ul class="tag-list" aria-label="Research methods">
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<li>Brain immune profiling</li>
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<li>Single-cell RNA-seq</li>
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<li>Spectral flow cytometry</li>
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<li>Neuropathology</li>
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</ul>
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</div>
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</article>
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<article class="research-card reveal">
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<div class="card-number">02</div>
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<p class="card-label">Immune aging</p>
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<h3>CD8+ T cells in age-related disease</h3>
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<p>My work contributes to understanding how clonally expanded memory CD8+ T-cell populations differ across aging, atherosclerosis, and neurovascular disease.</p>
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</article>
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<article class="research-card reveal">
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<div class="card-number">03</div>
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<p class="card-label">Vascular biology</p>
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<h3>Mitochondria and cardiovascular aging</h3>
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<p>I have examined how mitochondrial dysregulation, oxidative stress, and impaired quality control contribute to vascular decline across the lifespan.</p>
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</article>
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<article class="research-card reveal">
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<div class="card-number">04</div>
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<p class="card-label">Computational immunology</p>
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<h3>High-dimensional immune-cell analysis</h3>
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<p>I co-developed CAFÉ, an analysis pipeline and integrated web application designed to improve reproducible characterization of complex spectral flow cytometry data.</p>
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</article>
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</div>
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</div>
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</section>
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<section class="section" id="publications">
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<div class="shell">
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<div class="section-heading heading-row reveal">
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<div>
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<p class="section-kicker">Scholarship</p>
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<h2>Selected publications</h2>
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</div>
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<a class="text-link" href="https://scholar.google.com/citations?user=-qIZ0AgAAAAJ&hl=en" target="_blank" rel="noopener">View complete Google Scholar profile <span aria-hidden="true">↗</span></a>
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</div>
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<div class="publication-list">
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<article class="publication reveal">
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<div class="pub-year">2025</div>
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<div>
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<p class="pub-type">Bioinformatics · Research software</p>
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<h3>CAFÉ: an integrated web app for high-dimensional analysis and visualization in spectral flow cytometry</h3>
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<p>Md Hasanul Banna Siam, <strong>Md Akkas Ali</strong>, Donald Vardaman, Satwik Acharyya, Mallikarjun Patil, Daniel J. Tyrrell</p>
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<a href="https://doi.org/10.1093/bioinformatics/btaf176" target="_blank" rel="noopener">DOI: 10.1093/bioinformatics/btaf176</a>
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</div>
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</article>
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<article class="publication reveal">
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<div class="pub-year">2024</div>
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<div>
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<p class="pub-type">The Journal of Immunology · Co-first author</p>
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<h3>Development of a spectral flow cytometry analysis pipeline for high-dimensional immune cell characterization</h3>
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<p>Donald Vardaman III*, <strong>Md Akkas Ali*</strong>, Md Hasanul Banna Siam, et al.</p>
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<a href="https://doi.org/10.4049/jimmunol.2400370" target="_blank" rel="noopener">DOI: 10.4049/jimmunol.2400370</a>
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</div>
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</article>
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<article class="publication reveal">
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<div class="pub-year">2024</div>
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<div>
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<p class="pub-type">American Journal of Physiology–Heart and Circulatory Physiology · Review</p>
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<h3>Cardiovascular aging: spotlight on mitochondria</h3>
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<p><strong>Md Akkas Ali</strong>, Rachel Gioscia-Ryan, Daping Yang, Nicholas Sutton, Daniel J. Tyrrell</p>
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<a href="https://doi.org/10.1152/ajpheart.00632.2023" target="_blank" rel="noopener">DOI: 10.1152/ajpheart.00632.2023</a>
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</div>
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</article>
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<article class="publication reveal">
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<div class="pub-year">2024</div>
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<div>
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<p class="pub-type">Circulation · Conference abstract</p>
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<h3>Age-associated CD8+ T cells accumulate in the aging brain</h3>
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<p><strong>Md Akkas Ali</strong>, Donald Vardaman, Christina Bolding, et al.</p>
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<a href="https://doi.org/10.1161/circ.150.suppl_1.4146396" target="_blank" rel="noopener">DOI: 10.1161/circ.150.suppl_1.4146396</a>
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</div>
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</article>
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<article class="publication reveal">
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<div class="pub-year">2024</div>
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<div>
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<p class="pub-type">bioRxiv · Preprint</p>
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<h3>Tissue-resident memory CD8+ T cells are present but not critical for demyelination and neurodegeneration in a mouse model of multiple system atrophy</h3>
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<p>Nicholas J. Corbin-Stein, et al., <strong>Md Akkas Ali</strong>, et al.</p>
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<a href="https://doi.org/10.1101/2024.06.02.597035" target="_blank" rel="noopener">DOI: 10.1101/2024.06.02.597035</a>
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</div>
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</article>
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<article class="publication reveal">
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<div class="pub-year">2023</div>
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<div>
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<p class="pub-type">Nature Aging · Original research</p>
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<h3>Clonally expanded memory CD8+ T cells accumulate in atherosclerotic plaques and are pro-atherogenic in aged mice</h3>
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<p>Daniel J. Tyrrell, Kyle M. Wragg, Jiajia Chen, et al., <strong>Md Akkas Ali</strong>, et al.</p>
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<a href="https://doi.org/10.1038/s43587-023-00515-w" target="_blank" rel="noopener">DOI: 10.1038/s43587-023-00515-w</a>
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</div>
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</article>
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</div>
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</div>
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</section>
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<section class="section section-dark" id="experience">
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<div class="shell">
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<div class="section-heading reveal">
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<p class="section-kicker">Training and experience</p>
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<h2>From biotechnology and teaching to neuroimmune discovery.</h2>
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</div>
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<div class="timeline">
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<article class="timeline-item reveal">
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<div class="timeline-date">2023–Present</div>
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<div><h3>Graduate Research Assistant</h3><p>Department of Pathology, University of Alabama at Birmingham · Advisor: Daniel J. Tyrrell, PhD</p></div>
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</article>
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<article class="timeline-item reveal">
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<div class="timeline-date">2022–2023</div>
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<div><h3>Graduate Blazer Fellow</h3><p>University of Alabama at Birmingham</p></div>
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</article>
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<article class="timeline-item reveal">
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<div class="timeline-date">2018–2022</div>
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<div><h3>Faculty, Genetic Engineering and Biotechnology</h3><p>Shahjalal University of Science and Technology, Bangladesh · Lecturer and Assistant Professor roles</p></div>
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</article>
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<article class="timeline-item reveal">
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<div class="timeline-date">2015–2018</div>
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<div><h3>Biotech Executive</h3><p>Healthcare Pharmaceuticals Limited, Bangladesh</p></div>
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</article>
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</div>
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<div class="education-grid">
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<div class="education-card reveal"><span>Expected 2027</span><h3>PhD Candidate</h3><p>University of Alabama at Birmingham</p></div>
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<div class="education-card reveal"><span>2013</span><h3>MS, Genetic Engineering & Biotechnology</h3><p>Shahjalal University of Science and Technology</p></div>
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<div class="education-card reveal"><span>2011</span><h3>BSc, Genetic Engineering & Biotechnology</h3><p>Shahjalal University of Science and Technology</p></div>
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</div>
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</div>
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</section>
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<section class="section" id="presentations">
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<div class="shell two-column">
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<div class="section-sticky reveal">
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<p class="section-kicker">Scientific communication</p>
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<h2>Selected presentations</h2>
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<p>Public conference abstracts and invited presentations documented in my AHA biosketch.</p>
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</div>
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<div class="stack-list">
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<article class="stack-item reveal"><span>2025</span><div><h3>Age-Associated CD8+ T Cells Accumulate in the Aging Brain</h3><p>American Association of Immunologists Annual Meeting · Honolulu, Hawaii</p></div></article>
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<article class="stack-item reveal"><span>2024</span><div><h3>Age-Associated CD8+ T Cells Accumulate in the Aging Brain</h3><p>American Heart Association Scientific Sessions · Chicago, Illinois</p></div></article>
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<article class="stack-item reveal"><span>2024</span><div><h3>Exploring the Role of CD8+ T Cells in Vascular Dementia and Aging</h3><p>Invited presentation · MD Anderson Cancer Center</p></div></article>
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<article class="stack-item reveal"><span>2024</span><div><h3>Age-Associated CD8+ T Cells in the Aging Brain</h3><p>McKnight Brain Research Foundation Annual Meeting and Southeastern Immunology Symposium</p></div></article>
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</div>
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</div>
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</section>
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<section class="section recognition" id="recognition">
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<div class="shell recognition-grid">
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<div class="recognition-image reveal">
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<img src="https://lh3.googleusercontent.com/sitesv/AG8ngQUIIOwh77FHhkiyuiEtstmKynPoF6e8jqcCv3zGEWT-RBy1T-UpxRKzRQhvRTGApufxdLdUy5ZMnO-H93VE-MCBBt5nmgGOhVTTEHFSiH2JzIS5YTGIFUjHdxtB6jxFWm1x9oIP9yeShYef_6WnQobWt5a8A8WENPX0n3R6PapdUW5Ki0hLwS9RKZTV9rcD1expFs4puhHSldGXT4pk8HUJVJDm7uzDMGmFRyUFun0=w1280" alt="MD Akkas Ali holding the UAB Commitment to Community Engagement Award" width="1280" height="1834" loading="lazy">
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<p>Commitment to Community Engagement Award, UAB</p>
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</div>
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<div class="reveal">
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<p class="section-kicker">Leadership and recognition</p>
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<h2>Service across science and community.</h2>
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<p class="recognition-lede">My professional service includes leadership in COVID-19 diagnostic testing, international student engagement, and scientific communication.</p>
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<ul class="award-list">
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<li><span>2025</span><strong>Guest Speaker, Next-Generation DNA Sequencing Methods, UAB</strong></li>
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<li><span>2024</span><strong>UAB Pathology Travel Award</strong></li>
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<li><span>2024</span><strong>Invited Speaker, MD Anderson Cancer Center</strong></li>
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<li><span>2023</span><strong>Commitment to Community Engagement Award, UAB</strong></li>
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<li><span>2023</span><strong>Student Excellence Award, UAB</strong></li>
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<li><span>2022</span><strong>National recognition for COVID-19 diagnostic leadership</strong></li>
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<li><span>2021</span><strong>National Science and Technology Fellowship, Bangladesh</strong></li>
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</ul>
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</div>
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</div>
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</section>
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<section class="contact-section" id="contact">
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<div class="shell contact-grid">
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<div>
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<p class="section-kicker">Contact</p>
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<h2>Let’s connect around aging, immunity, and brain health.</h2>
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</div>
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<div>
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<p>I welcome conversations about neuroimmunology, vascular dementia, high-dimensional immune profiling, and collaborative research.</p>
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<a class="button button-light" href="mailto:mali3@uab.edu">mali3@uab.edu</a>
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<div class="social-links">
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<a href="https://scholar.google.com/citations?user=-qIZ0AgAAAAJ&hl=en" target="_blank" rel="noopener">Google Scholar</a>
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<a href="https://github.com/mdakkasali/" target="_blank" rel="noopener">GitHub</a>
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<a href="https://orcid.org/0000-0002-3626-3393" target="_blank" rel="noopener">ORCID</a>
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<a href="https://sites.uab.edu/tyrrelllab/people/" target="_blank" rel="noopener">Tyrrell Lab</a>
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</div>
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</div>
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</div>
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</section>
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</main>
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<footer class="site-footer">
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<div class="shell footer-inner">
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<p>© <span id="year"></span> MD Akkas Ali</p>
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<p>Neuroimmunology · Brain aging · Vascular dementia</p>
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<a href="#top">Back to top ↑</a>
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</div>
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</footer>
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<script src="script.js"></script>
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</body>
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</html>

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